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Currently pandora has two models allowed for kmer coverage distribution: negative binomial and binomial (approx poisson). Default is negative binomial.
In https://github.com/rmcolq/pandora/blob/7ad…
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Hi,
we recently sequenced a batch of 19 fungal isolates. I tried to assemble the genomes a few different ways (simplex + duplex or simplex corrected only) in order to figure out if there is still a…
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Hello,
I work with small marine animals and I have generated five single HiFi libraries from the same species. To avoid issues with the assemblies (heterozigosity, different haplotypes), I decided …
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Hi
When I run the BayesTyper v1.4, I got this error. Could anyone please help me to fix this? Thanks
[14/02/2019 06:13:18] You are using BayesTyper (v1.4)
[14/02/2019 06:13:18] Seeding pseudo…
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Hi,
I am using Bayestyper to genotype my yeast strains after the clustering step but I'm getting an assertion failure error. I ran `bayestyper genotype` with the --noise-genotyping parameter due to…
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Okay , i ran braken-build but get error, anz hint please what is wrong?
```
bracken-build -d kraken.NCBI.nt -t 32 -l 150 -x kraken.NCBI.nt -y kraken2
bracken -d kraken.NCBI.nt -i kraken.repo…
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Hi,
I want to plot kmer values of direct RNA sequenced samples, and got it to work successfully, but it appears that C and U center bases have the lowest signal, while A and G center nucleotides h…
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Hello,
Would it be possible to have the final confidence score reported in the output for each read? I'm exploring the use of this metric in calculating summary statistics for classified taxa (scor…
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Hi,
I am using Bayestyper to genotype SNPs of HG002 but I'm getting an assertion failure error. The reference SNPs are fetched from file processed by GIAB using freebayes.
The commands I used a…
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One noticeable difference between CORTEX and VARI is that CORTEX maintains coverage information. I'm wondering if there is an intelligent way to succinctly represent coverage. Ideally, this would ma…